EP4008340A1 - Compositions pour le traitement de la maladie c liaque - Google Patents

Compositions pour le traitement de la maladie c liaque Download PDF

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EP4008340A1
EP4008340A1 EP21167722.4A EP21167722A EP4008340A1 EP 4008340 A1 EP4008340 A1 EP 4008340A1 EP 21167722 A EP21167722 A EP 21167722A EP 4008340 A1 EP4008340 A1 EP 4008340A1
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residue
seq
amino acid
acid sequence
viii
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Justin Bloomfield Siegel
David Baker
Ingrid Swanson Pultz
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University of Washington Center for Commercialization
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University of Washington Center for Commercialization
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/52—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from bacteria or Archaea
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • C12N9/6489—Metalloendopeptidases (3.4.24)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y304/00—Hydrolases acting on peptide bonds, i.e. peptidases (3.4)
    • C12Y304/21—Serine endopeptidases (3.4.21)
    • C12Y304/21048—Cerevisin (3.4.21.48)

Definitions

  • Celiac sprue is a highly prevalent disease in which dietary proteins found in wheat, barley, and rye products known as 'glutens' evoke an immune response in the small intestine of genetically predisposed individuals. The resulting inflammation can lead to the degradation of the villi of the small intestine, impeding the absorption of nutrients. Symptoms can appear in early childhood or later in life, and range widely in severity, from diarrhea, fatigue and weight loss to abdominal distension, anemia, and neurological symptoms. There are currently no effective therapies for this lifelong disease except the total elimination of glutens from the diet. Although celiac sprue remains largely underdiagnosed, its' prevalence in the US and Europe is estimated at 0.5-1.0% of the population. The identification of suitable naturally-occurring enzymes as oral therapeutics for celiac disease is difficult due to the stringent physical and chemical requirements to specifically and efficiently degrade gluten-derived peptides in the harsh and highly acidic environment of the human digestive tract.
  • the invention provides methods for treating celiac sprue, comprising administering to a subject with celiac sprue an amount effective to treat the celiac sprue of one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOS: 75, 74, 76-89, 95, 97-98, 102-111, or processed versions thereof.
  • the one or more polypeptides comprise one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOs: 75, 74, 77, 78, 82, 88, 98, 105, 111, or processed versions thereof.
  • the one or more polypeptides comprise a polypeptide with the amino acid sequence of SEQ ID NO: 89.
  • the invention provides isolated polypeptides selected from the group consisting of the following polypeptides, or processed versions thereof:
  • the invention provides nucleic acids encoding the polypeptides of the invention, nucleic acid expression vectors comprising the isolated nucleic acids of the invention, and recombinant host cells comprising the nucleic acid expression vectors of the invention.
  • compositions comprising
  • the invention provides pharmaceutical compositions, comprising the isolated polypeptides, nucleic acids, expression vectors, host cells, or compositions of the invention, together with a pharmaceutically acceptable carrier.
  • amino acid residues are abbreviated as follows: alanine (Ala; A), asparagine (Asn; N), aspartic acid (Asp; D), arginine (Arg; R), cysteine (Cys; C), glutamic acid (Glu; E), glutamine (Gln; Q), glycine (Gly; G), histidine (His; H), isoleucine (Ile; I), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V).
  • the present invention provides methods for treating celiac sprue, comprising administering to a subject with celiac sprue an amount effective to treat the celiac sprue of one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of the following, or processed versions thereof:
  • the polypeptides disclosed herein are Kumamolisin homologue polypeptides and modified versions thereof that have been identified as having similar, improved, or complementary activity compared to Kumamolisin-As in hydrolyzing proline (P)- and glutamine (Q)-rich components of gluten known as 'gliadins' believed responsible for the bulk of the immune response in most celiac sprue patients. Numerous other Kumamolisin homologues tested by the inventors possessed little or no such gliadin hydrolyzing activity. Thus, the polypeptides disclosed herein can be used to treat celiac sprue.
  • the amino acid sequences disclosed herein are for the preprocessed version of the polypeptides, which may hydrolyze their substrates in a processed form. Thus, use of the processed versions of the polypeptides are covered herein. As will be understood by those of skill in the art, the exact processing of the polypeptides may differ from one cell type or set of conditions to another. In one embodiment, the processed forms of the homologues are devoid of the residues shown in Table 1 below, which is a comparison of the residues of Kummamolisin and the homologues disclosed herein that are present in the pre-processed form but not in the processed form.
  • the one or more polypeptides are selected from the group consisting of the following, or processed versions thereof
  • the one or more polypeptides comprise one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOs: 74, 75, 77, 78, 82, 88, 98, 105, 111, or processed versions thereof.
  • the one or more polypeptides comprise a polypeptide that comprises or consists of the amino acid sequence: Homologue 4 mutant
  • the methods may comprise administration of the one or more polypeptides together with any other suitable active agent to treat celiac sprue.
  • the methods further comprise administering to the subject an amount of one or more further polypeptides comprising an amino acid sequence selected from the group consisting of:
  • the one or more further polypeptides have been disclosed for use in treating celiac sprue (see WO2013/023151 ).
  • the further polypeptides are either the processed version of Kumamolisin-As (SEQ ID NO:67) or the preprocessed version of Kumamolisin-As (SEQ ID NO:33), or modified versions thereof, which are known as a member of the sedolisin family of serine-carboxyl peptidases, and utilizes the key catalytic triad Ser 278 -Glu 78 -Asp 32 in its processed form to hydrolyze its substrate (Ser 467 -Glu 267 -Asp 271 in the pre-processed form) Its maximal activity is at pH ⁇ 4.0.
  • the further polypeptides may comprise one or more amino acid changes from SEQ ID NO: 67 (wild type processed Kumamolisin-As) at one or more residues selected from the group consisting of residues 73, 102, 103, 104, 130, 165, 168, 169, 172, and 179 (numbering based on the wild type processed Kumamolisin-As amino acid sequence).
  • the one or more changes relative to the wild type processed Kumamolisin-As amino acid sequence may be selected from the group consisting of: Wild type Residue# AA change S73 K, G N102 D T103 S D104 A, T, N G130 S S165 N T168 A D169 N, G Q172 D D179 S, H
  • the one or more changes relative to the wild type processed Kumamolisin-As amino acid sequence may include at least N102D. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least N102D and D169N or D169G. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least N102D, D169G, and D179H. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least S73K, D104T, N102D, G130S, D169G, and D179H.
  • the further polypeptides may comprise one or more amino acid changes from SEQ ID NO: 33 (wild type pre-processed Kumamolisin-As) at one or more residues selected from the group consisting of residues 119, 262, 291, 292, 293, 319, 354, 357, 358, 361, and 368 (numbering based on the wild type pre-processed Kumamolisin-As amino acid sequence).
  • the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may be selected from the group consisting of: Wild type Residue# AA change V119 D S262 K, G N291 D T292 S D293 A, T, N G319 S S354 N T357 A D358 N, G Q361 D D368 S, H
  • the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least N291D. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least N291D and 358N or 358G. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least N291D, 358G, and 368H. In another embodiment the one or more changes relative to the wild type Kumamolisin-As amino acid sequence may include at least V119D, S262K, D293T, N291D, G319S, D358G, and D368H.
  • polypeptide differs in its full length amino acid sequence by 25% or less (including any amino acid substitutions, deletions, additions, or insertions) from the polypeptide defined by SEQ ID NO:1 or 35.
  • the one or more further polypeptides comprise or consist of an amino acid sequence at least 75% identical to any one of SEQ ID NOS:2-33 or 36-67, or, alternatively, 2-32 or 36-66.
  • the polypeptides represented by these SEQ ID NOS are specific examples of polypeptides with improved protease activity at pH 4 against the oligopeptide PQPQLP (SEQ ID NO: 34) (a substrate representative of gliadin) compared to wild type Kumamolisin-As.
  • the one or more further polypeptides comprise or consist of an amino acid sequence at least 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence according to any one of SEQ ID NOS:36-66.
  • the one or more polypeptides comprise or consist of an amino acid sequence according to any one of SEQ ID NOS: 2-33 or 36-67 or, alternatively, 2-32 or 36-66.
  • the one or more further polypeptide comprises or consists of a polypeptide comprising the amino acid sequence shown below (KumaMax TM ): MSDMFXPWKEGEEARAVLQGHARAQAPQAVDKGPVAGDERMAVTVVLRRQRAG ELAAHVERQAAIAPHAREHLKREAFAASHGASLDDFAELRRFADAHGLALDRANVA AGTAVLSGPDDAINRAFGVELRHFDHPDGSYRSYLGEVTVPASIAPMIEAVLGLDTR PVARPHFRMQRRAEGGFEARSQAAAPTAYTPLDVAQAYQFPEGLDGQGQCIAIIELG GGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPKGPDGEVELDIEVAGALA PGAKFAVYFAPDTTAGFLDAITTAIHDPTLKPSVVSISWSGPEDSWTSAAIAAMNRAF LDAAALGVTVLAAAGDSGSTGGEQDGLYHVHFPAASPYVLACGGTRLVASG
  • the method comprises administering Homologue 4 or full length mutant Homologue 4 (SEQ ID NOs: 75, 89, and/or 98), or processed versions thereof, together with the one or more of the further polypeptides disclosed herein, including but not limited to KumaMa TM x (SEQ ID NO: 90), or a processed version thereof.
  • Homologue 4 SEQ ID NO: 98
  • has increased activity against ⁇ -gliadin peptide amino acid sequence IQPQQPAQL (SEQ ID NO: 92)
  • Kumamolisin polypeptides amino acid sequence IQPQQPAQL
  • administering may provide an improved therapy for gluten digestion.
  • Homologue 4 SEQ ID NO: 98
  • one or more Kumamolisin polypeptides such as KumaMax TM (SEQ ID NO: 90), or a processed version thereof
  • KumaMax TM SEQ ID NO: 90
  • the Homologue 4 polypeptide comprises or consists of the full length Hom 4 mutant (SEQ ID NO: 89) or a processed version thereof, which is shown in the examples below to provide significantly improved activity against degradation products of gluten in the stomach that have been specifically linked to celiac disease: the 33mer peptide (LQLQPFPQPQLPYPQPQLPYPQPQLPYPQPQPF (SEQ ID NO: 72)) and the 26mer peptide (FLQPQQPFPQQPQQPYPQQPQPFPQ (SEQ ID NO: 73)).
  • the method comprises administering Homologue 1 (SEQ ID NO: 74), Homologue 6 (SEQ ID NO: 77), and/or the Homologue 6 mutant (SEQ ID NO: 78), or processed versions thereof, together with the one or more of the further polypeptides disclosed herein, including but not limited to KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • Homologue 1 SEQ ID NO: 74
  • Homologue 6 mutant demonstrates optimal activity at a pH level below that of the other homologues and the further Kumamolisin related polypeptides.
  • Homologue 1 SEQ ID NO: 74
  • Homologue 6 SEQ ID NO: 77
  • Homologue 6 mutant SEQ ID NO: 78
  • processed versions thereof can be used alone in appropriate pH environments, or used in combination with the one or more further polypeptides to expand the pH profile of the one or more further polypeptides, to for example, more accurately mimic the pH of the stomach.
  • the method comprises administering Homologue 26 (SEQ ID NO: 88 or 111) or a processed version thereof, together with the one or more further polypeptides, including but not limited to KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • Homologue 26 SEQ ID NO:111
  • has very strong activity in breaking down the 33mer gliadin peptide and thus can be used for treating celiac sprue disease, either alone or on combination with the one or more further polypeptides, including but not limited to KumaMax TM (SEQ ID NO: 90).
  • Celiac sprue also known as celiac disease or gluten intolerance
  • celiac disease or gluten intolerance is a highly prevalent disease in which dietary proteins found in wheat, barley, and rye products known as 'glutens' evoke an immune response in the small intestine of genetically predisposed individuals. The resulting inflammation can lead to the degradation of the villi of the small intestine, impeding the absorption of nutrients.
  • Symptoms can appear in early childhood or later in life, and range widely in severity, from diarrhea, fatigue, weight loss, abdominal pain, bloating, excessive gas, indigestion, constipation, abdominal distension, nausea/vomiting, anemia, bruising easily, depression, anxiety, growth delay in children, hair loss, dermatitis, missed menstrual periods, mouth ulcers, muscle cramps, joint pain, nosebleeds, seizures, tingling or numbness in hands or feet, delayed puberty, defects in tooth enamel, and neurological symptoms such as ataxia or paresthesia.
  • There are currently no effective therapies for this lifelong disease except the total elimination of glutens from the diet.
  • celiac sprue remains largely underdiagnosed, its' prevalence in the US and Europe is estimated at 0.5-1.0% of the population.
  • treating celiac sprue means accomplishing one or more of the following: (a) reducing the severity of celiac sprue; (b) limiting or preventing development of symptoms characteristic of celiac sprue; (c) inhibiting worsening of symptoms characteristic of celiac sprue; (d) limiting or preventing recurrence of celiac sprue in patients that have previously had the disorder; (e) limiting or preventing recurrence of symptoms in patients that were previously symptomatic for celiac sprue; and (f) limiting development of celiac sprue in a subject at risk of developing celiac sprue, or not yet showing the clinical effects of celiac sprue.
  • the subject to be treated according to the methods of the invention may be any subject suffering from celiac sprue, including human subjects.
  • the subject may be one already suffering from symptoms or one who is asymptomatic.
  • the subject may have an HLA-DQ2 serotype; in another embodiment, the subject may have an HLA-DQA serotype.
  • Polypeptides with increased activity against ⁇ -gliadin (Homologues 1, 4, 5, and 9 (SEQ ID NOs: 74, 75, 76, 79, 89, 98, 99, and 102)) may be particularly useful for treating subjects with an HLA-DQ8 serotype.
  • Polypeptides with increased activity against ⁇ 2-gliadin and ⁇ 9-gliadin and/or the 33-mer and 26-mer degradation products of gluten described herein may be particularly useful for treating subjects with an HLA-DQ2 serotype.
  • an “amount effective” refers to an amount of the polypeptide that is effective for treating celiac sprue.
  • the polypeptides are typically formulated as a pharmaceutical composition, such as those disclosed above, and can be administered via any suitable route, including orally, parentally, by inhalation spray, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles.
  • the pharmaceutical compositions and formulations are orally administered, such as by tablets, pills, lozenges, elixirs, suspensions, emulsions, solutions, or syrups.
  • Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response).
  • a suitable dosage range may, for instance, be 0.1 ug/kg-100 mg/kg body weight; alternatively, it may be 0.5 ug/kg to 50 mg/kg; 1 ug/kg to 25 mg/kg, or 5 ug/kg to 10 mg/kg body weight.
  • the polypeptides can be delivered in a single bolus, or may be administered more than once (e.g., 2, 3, 4, 5, or more times) as determined by an attending physician.
  • the present invention provides isolated polypeptides selected from the group consisting of the following polypeptides, or processed versions thereof.
  • polypeptides may be processed versions of the recited polypeptides; the presently claimed polypeptides include any such processed versions of the recited polypeptides. Processed versions of the polypeptides are as defined above.
  • the isolated polypeptide comprises the amino acid sequence of a polypeptide selected from Homologues 4, Homolog 6 mutant, and Homologs 13 and 26, or processed versions thereof. In another embodiment, the isolated polypeptide comprises the amino acid sequence of Hom 4 mutant:
  • the polypeptides disclosed herein have been identified as having similar, improved, or complementary activity compared to Kumamolisin-related poypeptides in hydrolyzing proline (P)- and glutamine (Q)-rich components of gluten known as 'gliadins' believed responsible for the bulk of the immune response in most celiac sprue patients. Numerous other Kumamolisin homologues tested by the inventors possessed little or no such gliadin hydrolyzing activity. Thus, the polypeptides can be used to treat celiac sprue.
  • the polypeptides of this aspect of the invention degrade gliadins at various pHs. Such degradation occurs under the conditions disclosed in the examples that follow.
  • polypeptide is used in its broadest sense to refer to a sequence of subunit amino acids, whether naturally occurring or of synthetic origin.
  • the polypeptides of the invention may comprise L-amino acids, D-amino acids (which are resistant to L-amino acid-specific proteases in vivo), or a combination of D- and L-amino acids.
  • the polypeptides described herein may be chemically synthesized or recombinantly expressed.
  • the polypeptides may be linked to other compounds to promote an increased half-life in vivo, such as by PEGylation, HESylation, PASylation, or glycosylation.
  • polypeptides may be linked to any other suitable linkers, including but not limited to any linkers that can be used for purification or detection (such as FLAG or His tags).
  • compositions comprising
  • the one or more further polypeptides can be any as described above.
  • the one or more further polypeptides may comprise or consist of an amino acid sequence at least 75%, 80%, 85%, 90%, 95%, or 100% identical to any one of SEQ ID NOS:2-33 or 36-67, or, alternatively, 2-32 or 36-66.
  • the one or more further polypeptides comprise or consist of KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • the composition comprises Homologue 4 (SEQ ID NO: 75 or 98) or full length mutant Homologue 4 (SEQ ID NO: 89), or processed versions thereof, together with the one or more of the further polypeptides disclosed herein, including but not limited to KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • the composition comprises SEQ ID NO: 74, SEQ ID NO: 77, and/or SEQ ID NO: 78 (Homologue 1, Homologue 6, and/or the Homologue 6 mutant), or processed versions thereof, together with the one or more of the further polypeptides disclosed herein, including but not limited to KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • the method comprises administering SEQ ID NO: 88 and/or 111 (Homologue 26) or a processed version thereof, together with the one or more further polypeptides, including but not limited to KumaMax TM (SEQ ID NO: 90), or a processed version thereof.
  • the present invention provides isolated nucleic acids encoding the polypeptide of any aspect or embodiment of the invention.
  • the isolated nucleic acid sequence may comprise RNA or DNA.
  • isolated nucleic acids are those that have been removed from their normal surrounding nucleic acid sequences in the genome or in cDNA sequences.
  • Such isolated nucleic acid sequences may comprise additional sequences useful for promoting expression and/or purification of the encoded protein, including but not limited to polyA sequences, modified Kozak sequences, and sequences encoding epitope tags, export signals, and secretory signals, nuclear localization signals, and plasma membrane localization signals. It will be apparent to those of skill in the art, based on the teachings herein, what nucleic acid sequences will encode the polypeptides of the invention.
  • the present invention provides nucleic acid expression vectors comprising the isolated nucleic acid of any embodiment of the invention operatively linked to a suitable control sequence.
  • “Recombinant expression vector” includes vectors that operatively link a nucleic acid coding region or gene to any control sequences capable of effecting expression of the gene product.
  • "Control sequences" operably linked to the nucleic acid sequences of the invention are nucleic acid sequences capable of effecting the expression of the nucleic acid molecules. The control sequences need not be contiguous with the nucleic acid sequences, so long as they function to direct the expression thereof.
  • intervening untranslated yet transcribed sequences can be present between a promoter sequence and the nucleic acid sequences and the promoter sequence can still be considered "operably linked" to the coding sequence.
  • Other such control sequences include, but are not limited to, polyadenylation signals, termination signals, and ribosome binding sites.
  • Such expression vectors can be of any type known in the art, including but not limited plasmid and viral-based expression vectors.
  • control sequence used to drive expression of the disclosed nucleic acid sequences in a mammalian system may be constitutive (driven by any of a variety of promoters, including but not limited to, CMV, SV40, RSV, actin, EF) or inducible (driven by any of a number of inducible promoters including, but not limited to, tetracycline, ecdysone, steroid-responsive).
  • inducible promoters including, but not limited to, tetracycline, ecdysone, steroid-responsive.
  • the expression vector must be replicable in the host organisms either as an episome or by integration into host chromosomal DNA.
  • the expression vector comprises a plasmid.
  • the invention is intended to include other expression vectors that serve equivalent functions, such as viral vectors.
  • the present invention provides recombinant host cells comprising the nucleic acid expression vectors of the invention.
  • the host cells can be either prokaryotic or eukaryotic.
  • the cells can be transiently or stably transfected or transduced.
  • Such transfection and transduction of expression vectors into prokaryotic and eukaryotic cells can be accomplished via any technique known in the art, including but not limited to standard bacterial transformations, calcium phosphate co-precipitation, electroporation, or liposome mediated-, DEAE dextran mediated-, polycationic mediated-, or viral mediated transfection.
  • a method of producing a polypeptide according to the invention is an additional part of the invention.
  • the method comprises the steps of (a) culturing a host according to this aspect of the invention under conditions conducive to the expression of the polypeptide, and (b) optionally, recovering the expressed polypeptide.
  • the expressed polypeptide can be recovered from the cell free extract, cell pellet, or recovered from the culture medium. Methods to purify recombinantly expressed polypeptides are well known to the man skilled in the art.
  • the present invention provides pharmaceutical compositions, comprising the polypeptide, nucleic acid, nucleic acid expression vector, the recombinant host cell, or composition of any aspect or embodiment of the invention, together with a pharmaceutically acceptable carrier.
  • the pharmaceutical compositions of the invention can be used, for example, in the methods of the invention described below.
  • the pharmaceutical composition may comprise in addition to the polypeptides, nucleic acids, etc. of the invention (a) a lyoprotectant; (b) a surfactant; (c) a bulking agent; (d) a tonicity adjusting agent; (e) a stabilizer; (f) a preservative and/or (g) a buffer.
  • the buffer in the pharmaceutical composition is a Tris buffer, a histidine buffer, a phosphate buffer, a citrate buffer or an acetate buffer.
  • the pharmaceutical composition may also include a lyoprotectant, e.g. sucrose, sorbitol or trehalose.
  • the pharmaceutical composition includes a preservative e.g.
  • the pharmaceutical composition includes a bulking agent, like glycine.
  • the pharmaceutical composition includes a surfactant e.g., polysorbate-20, polysorbate-40, polysorbate- 60, polysorbate-65, polysorbate-80 polysorbate-85, poloxamer-188, sorbitan monolaurate, sorbitan monopalmitate, sorbitan monostearate, sorbitan monooleate, sorbitan trilaurate, sorbitan tristearate, sorbitan trioleate, or a combination thereof.
  • the pharmaceutical composition may also include a tonicity adjusting agent, e.g., a compound that renders the formulation substantially isotonic or isoosmotic with human blood.
  • Exemplary tonicity adjusting agents include sucrose, sorbitol, glycine, methionine, mannitol, dextrose, inositol, sodium chloride, arginine and arginine hydrochloride.
  • the pharmaceutical composition additionally includes a stabilizer, e.g., a molecule which, when combined with a protein of interest substantially prevents or reduces chemical and/or physical instability of the protein of interest in lyophilized or liquid form.
  • Exemplary stabilizers include sucrose, sorbitol, glycine, inositol, sodium chloride, methionine, arginine, and arginine hydrochloride.
  • polypeptides, nucleic acids, etc. of the invention may be the sole active agent in the pharmaceutical composition, or the composition may further comprise one or more other active agents suitable for an intended use.
  • compositions described herein generally comprise a combination of a compound described herein and a pharmaceutically acceptable carrier, diluent, or excipient. Such compositions are substantially free of non-pharmaceutically acceptable components, i.e. , contain amounts of non-pharmaceutically acceptable components lower than permitted by US regulatory requirements at the time of filing this application.
  • the composition if the compound is dissolved or suspended in water, the composition further optionally comprises an additional pharmaceutically acceptable carrier, diluent, or excipient.
  • the pharmaceutical compositions described herein are solid pharmaceutical compositions (e.g ., tablet, capsules, etc .).
  • compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by any suitable route.
  • the pharmaceutical compositions and formulations are designed for oral administration.
  • Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • compositions can be in any suitable form, including but not limited to tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, sterile injectable solutions, and sterile packaged powders.
  • Celiac disease is an autoimmune disorder that afflicts approximately 1% of the population (1, 2). This disease is characterized by an inflammatory reaction to gluten, the major protein in wheat flour, and to related proteins in barley and rye (2).
  • Gluten is composed of a heterogeneous mixture of the glycoproteins gliadin and glutenin (3).
  • ⁇ -gliadin is partially degraded by gastric and intestinal proteases to oligopeptides, which are resistant to further proteolysis due to their unusually high proline and glutamine content (3).
  • Immunogenic oligopeptides that result from incomplete proteolysis are enriched in the PQ motif (4, 5), which stimulate inflammation and injury in the intestine of people with Celiac disease.
  • the only treatment for this disease is complete elimination of gluten from the diet, which is difficult to attain due to the ubiquity of this protein in modern food products (6).
  • Oral enzyme therapy in which orally administered proteases are employed to hydrolyze immunogenic peptides before they are capable of triggering inflammation is currently being explored as a treatment for gluten intolerance.
  • proteases have been considered due to their specificity for cleavage after either proline or glutamine residues.
  • these enzymes often demonstrate characteristics that hinder their use in OET for gluten degradation.
  • Most of these peptidases exhibit optimal catalytic activity at neutral pH; however, the pH of the human stomach ranges from 2 to 4. These enzymes are therefore most active when they reach the pH-neutral small intestine, which is too late for effective prevention of Celiac disease as this is the site where gluten-derived pathology develops.
  • several of these enzymes demonstrate instability in the low pH of the human stomach, are susceptible to proteolysis by digestive proteases, or require extensive refolding procedures during their purification, which are all characteristics that hamper efforts for clinical use.
  • the ideal protease for the application of OET in the treatment of gluten intolerance would combine the following traits: optimal activity at low pH, easy purification, stability under the conditions of the human stomach, and high specificity for amino acid motifs found in gluten-derived immunogenic oligopeptides.
  • KumaMax TM An exemplary computationally designed enzyme, designated KumaMax TM , exhibited over 100-fold increased proteolytic activity and an 800-fold switch in substrate specificity for the targeted PQ motif compared to wild-type KumaWT.
  • KumaMax TM demonstrates resistance to common gastric proteases and is produced at high yields in E. coli without the need for refolding.
  • the inventors tested a large number of Kumamolisin homologues obtained from a wide variety of organisms for activity in degrading gliadin proteins. They share the catalytic triad present in Kumamolisin-As (Ser 467 -Glu 267 -Asp 271 in the Kumamolisin-As pre-processed form).
  • the purified homologue were incubated with protein with purified peptides that represent the immunogenic regions throughout gliadin, which is the problematic fraction of gluten for celiac patients.
  • Homologues were assessed for their ability to break down a fluorescent analogue of gliadin, a hexapeptide (QPQLPY (SEQ ID NO: 91)) that was conjugated to a fluorophore and a quencher, in simulated lab gastric conditions (NaOAc buffer pH 4.0 at 37°C). The rate of degradation can be calculated from measurement of the fluorescence signal over time. The activity was compared to that of Kumamolisin (denoted below as KWT). Kumamolisin has some activity breaking down these gliadin substrates. Exemplary results are shown in Figure 1 . As can be noted, only a subset of the homologues (1, 2, 4, 8, and 9) tested had activity comparable to or better than Kumamolisin under these conditions.
  • Kumamolisin and KumaMax TM have fairly low levels of activity against the ⁇ -gliadin peptide, while Homologue 4 has increased activity against this peptide, suggesting that Homologue 4, alone or in combination therapy with Kumamolisin-related polypeptides, may be an effective therapy for gluten digestion.
  • KumaMax TM mutations in the homologues inspired us to make these three active-site mutations alone on the Kumamolisin background (note that KumaMax TM contains a total of 7 mutations from Kumamolisin, but only 3 are within the active site).
  • This mutant which only contains these active-site mutations, is called the K3 mutant below.
  • the data are provided in Table 4 and Figure 3 .
  • homologues 13 and 26 demonstrated significant activity against the 33mer peptide; see Figure 4 .
  • homologue 26 in its wild type form had very strong activity comparable to KumaMax TM at breaking down the 33mer peptide.
  • Homologue 4 SEQ ID NO:75
  • Homologue 4 mutant SEQ ID NO: 89
  • 13 and 26 can be used as therapeutics to treat celiac disease.
  • Homologue 26 SEQ ID NOL 88
  • KumaMax TM SEQ ID NO: 90
  • Homologue 4 demonstrated increased activity with the mutations that were made to KumaMax TM .
  • pH profiles from these homologues suggest that these homologues, alone or in combination, can expand the pH range of therapeutic efficacy in the human stomach.
  • 500 uL of the overnight culture was added to 500 mL autoinduction media (5 g tryptone, 2.5 g yeast extract, 465 mL ddH 2 O), and shaken at 37° C for roughly 4 hours, then the autoinduction components were added (500 uL MgSO 4 , 500 uL 1000x trace metals, 25 mL 20x NPS, 10 mL 20x 5052, 500 uL 50 mg/mL Kan). The cultures were then shaken at 18° C for 30 hours before being spun down.
  • autoinduction media 5 g tryptone, 2.5 g yeast extract, 465 mL ddH 2 O
  • Pellets were resuspended in 10 mL 1x PBS, then lysed via sonication with 5 mL lysis buffer (50 mM HEPES, 500 mM NaCl, 1 mM bME, 2 mg/mL lysozyme, 0.2 mg/mL DNase, ddH 2 O) and spun down. The proteins were then purified over 1mL TALON cobalt affinity columns.
  • 5 lysis buffer 50 mM HEPES, 500 mM NaCl, 1 mM bME, 2 mg/mL lysozyme, 0.2 mg/mL DNase, ddH 2 O
  • KumaMax, KumaWT, and SC Pep were washed three times with 20 mL wash buffer (10 mM imidazole, 50 mM HEPES, 500 mM NaCl, 1mM bME, ddH 2 O), and then eluted in 15 mL of elution buffer (200 mM imidazole, 50 mM HEPES, 500 mM NaCl, 1mM bME).
  • EP-B2 had to be refolded on the column, so after lysis the pellets were resuspended in 10 mL of EP-B2 buffer, which differs from the wash buffer only in that it is diluted in guanidine hydrochloride instead of ddH 2 O to allow for denaturation of the EP-B2 inclusion bodies. This resuspension was pelleted, and the supernatant (containing denatured EP-B2) was filtered with a 0.8 ⁇ m filter onto the column. EP-B2 was washed once with 20 mL of the EP-B2 buffer, before being washed twice with 20 mL of the wash buffer to refold the protein on the column.
  • Protein was eluted with 15 ml of the elution buffer. All proteins were concentrated from 15 mL down to ⁇ 500 uL, then dialyzed once in 1 L dialysis buffer (20% glycerol, 50 mM HEPES, 500 mM NaCl, 1 mM bME). Protein concentration was calculated spectrophotometrically with extinction coefficients of 53,985 M -1 cm -1 for Kuma WT and all Kuma WT variants, 152,290 M -1 cm -1 for SC Pep, and 58,245 M -1 cm -1 for EP-B2.
  • the variants of Kumamolisin-As that displayed the most activity on the FQ substrate in the activity screen were sequenced, then purified in small scale. 500 uL of TB+K an overnight cultures were added to 50 mL TB+K an and grown at 37° C until reaching an optical density of 0.5-0.8. IPTG was added to 0.5 mM, and the cultures were expressed at 22° C for 16-24 hours.
  • the cells were spun down, resuspended in 500 uL of wash buffer (1x PBS, 5 mM imidazole, ddH 2 O), transferred to a 2 mL Eppendorf tube, and lysed in 1 mL lysis buffer (1x PBS, 5 mM imidazole, 2x Bug Buster TM , 2 mg/mL lysozyme, 0.2 mg/mL DNase, ddH 2 O). After centrifugation, the supernatant was decanted into a fresh tube. Columns with 200 uL of TALON cobalt resin were placed in Eppendorf tubes, and the supernatant was poured over the columns and rocked for 20 minutes before spinning down and discarding the flow-through.
  • wash buffer (1x PBS, 5 mM imidazole, ddH 2 O
  • 1x PBS, 5 mM imidazole, 2x Bug Buster TM 2 mg/mL lysozyme, 0.2 mg/
  • the proteins were washed three times with 500 uL wash buffer, discarding the flow-through between washes. Enzymes were eluted in 200 uL elution buffer (1x PBS, 200 mM imidazole, dd H 2 O), and concentrations were calculated spectrophotometrically using an extinction coefficient of 53,985 M -1 cm -1 .
  • the Kurnamolisin-As mutants were incubated for 15 minutes in pH 4 100 mM sodium acetate buffer. Enzyme was added to 5 ⁇ M substrate so that the final protein concentration was 0.0125 mg/mL. The fluorescence was measured at 30-second intervals for 1 hour.
  • Enzyme variant proclivity for gluten degradation was measured by hydrolysis of the fluorescently quenched ⁇ -gliadin hexapeptide analogue QXL520-PQPQLP-K(5-FAM)-NH2 (FQ) (SEQ ID NO: 69) as a substrate. Each enzyme was incubated at room temperature for 15 minutes in 100 mM pH 4 sodium acetate buffer.
  • fluorescent substrate After 15 minutes, 50 uL of fluorescent substrate was added ranging in final concentration between 100, 50, 25, 12.5, 6.25, and 0 ⁇ M peptide, and maintaining concentrations of 0.05 ⁇ M KumaMax TM , 0.5 ⁇ M Kuma WT, 0.5 ⁇ M SC Pep, and 0.5 ⁇ M EP-B2 across all variations in substrate concentration.
  • the plate was read immediately on the spectrophotometer for an hour, using 455 nm wavelength for excitation and reading 485 nm wavelength for emission.
  • the enzymes were also tested for specificity to different dipeptide motifs using a variety of chromogenic substrates that release p-nitroaniline (pNA) upon hydrolysis: [Suc-APQ-pNA], [Suc-AQP-pNA], [Suc-APE-pNA], and [Suc-APR-pNA]. Again, each enzyme was incubated at room temperature for 15 minutes in 100 mM pH 4 sodium acetate buffer. After 15 minutes, 20 uL of substrate was added to the enzyme incubation so that the final concentrations of substrate ranged between 1000, 500, 250, 125, 62.5, 31.25, 15.625, and 0 ⁇ M, and all enzymes being tested ended in a concentration of 0.5 ⁇ M. The plate was read immediately on the spectrophotometer for an hour, monitoring absorption by the reactions at 385nm.
  • pNA p-nitroaniline
  • the standard curve for the fluorescent peptide involved mixing substrate and product together at varying concentrations in pH 4 buffer. Substrate concentrations were 100, 50, 25, 12.5, 6.25, and 0 ⁇ M, and product concentrations were 20, 5, 1.25, 0.3125, 0.078125, 0 ⁇ M.
  • the standard curve for the absorbent peptide involved product concentrations of 100, 50, 25, 12.5, 6.25, 3.125, 1.5625, 0.78125, 0.390625, 0.1953125, 0.09765625, and 0 ⁇ M diluted in pH 4 buffer.
  • Enzyme stability was determined in the presence the digestive proteases, pepsin and trypsin.
  • Kuma WT, KumaMax TM , SC Pep, and EP-B2 were incubated in buffer matching the native pH environment of each digestive protease. pH 3.5 100 mM sodium acetate was used to pre-incubate the enzymes for pepsin digestion assays, and pH 7.5 dialysis buffer (see "Protein Expression and Purification") for the trypsin digestion assays. Each experimental enzyme was incubated at 37° C for 15 minutes in each buffer, at a concentration of 0.2 mg/mL.
  • the rate of protein self-proteolysis was determined at pH 4 and 7.5 in the absence of pepsin or trypsin. Each enzyme, at a concentration of 0.2 mg/mL, was incubated in pH 4 100 mM sodium acetate and pH 7.5 dialysis buffer. At 20, 40, and 60 minutes, timepoints were taken. SDS was added, and the aliquots were boiled for 5 minutes to ensure denaturation of the enzymes and inhibition of further self-proteolysis. Again, an SDS-PAGE gel in conjunction with ImageJ allowed quantification of enzyme self-proteolysis.
  • Enzyme activity on full-length ⁇ 9-gliadin was measured using high-performance liquid-chromatography mass spectrometry.
  • 7 ⁇ L of pH 4 1M sodium acetate buffer was added to 28 ⁇ L of 5 ⁇ M enzyme, and incubated alongside separate tubes of 3 ⁇ L gliadin at 37° C for 15 minutes.
  • 27 ⁇ L of each enzyme mixture, and 27 ⁇ L of dialysis buffer as a control were added to each tube of gliadin. These were incubated once more at 37° C, and 5 ⁇ L samples were taken at 10, 20, 30, 40, and 50 minutes.
  • Each timepoint sample was quenched in 95 ⁇ L of 80% acetonitrile with 1% formic acid and approximately 33 ⁇ M leupeptin. The samples were analyzed on the HPLC to compare gliadin degradation by the different proteases over time.

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